Contacts of the helix formed by residues 848 - 863 (chain A) in PDB entry 5WBL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 848 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PRO* 4.1 10.7 - - - +
709A ARG* 4.1 1.6 - - - -
846A ASP* 3.0 16.3 + - - +
847A PRO* 1.3 71.5 - - - +
849A PRO* 1.3 68.6 - - - +
850A ARG* 4.2 5.4 + - - +
851A ILE* 2.8 46.0 + - - +
852A ALA* 3.0 8.4 + - - +
1112A LEU* 4.0 11.9 - - - +
1115A GLY 4.0 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A PRO 3.0 10.4 - - - +
848A SER* 1.3 84.9 - - - +
850A ARG* 1.3 58.8 + - + +
852A ALA* 3.4 10.5 - - + +
853A SER* 2.8 31.4 + - - -
856A ARG* 4.5 4.4 + - - +
1070A PHE* 6.2 1.8 - - + -
1099A ARG* 5.6 1.1 - - - +
1112A LEU* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 4.6 4.5 - - - +
88A GLY* 3.6 42.5 + - - -
710A ALA* 6.2 0.9 - - + -
848A SER* 3.0 3.9 + - - +
849A PRO* 1.3 77.8 - - + +
851A ILE* 1.3 71.6 + - + +
853A SER* 3.2 27.8 + - - -
854A LEU* 3.3 50.7 + - + +
962A PRO* 5.2 2.4 - - - +
963A LEU 5.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A PRO* 3.6 26.7 - - + +
709A ARG* 3.9 17.0 - - + +
710A ALA* 3.8 28.3 - - + +
713A ALA* 5.4 0.9 - - + -
843A LEU* 3.6 22.7 - - + +
846A ASP* 3.3 30.1 - - + +
848A SER* 2.8 31.5 + - - +
850A ARG* 1.3 76.6 - - + +
852A ALA* 1.3 66.6 + - - +
854A LEU* 3.2 9.5 + - - +
855A GLY* 3.0 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A LEU 3.3 11.4 - - - +
844A ALA* 3.6 12.5 - - - +
846A ASP* 3.6 21.3 - - - +
848A SER 3.0 4.4 + - - -
849A PRO* 3.4 13.5 - - + +
851A ILE* 1.3 76.8 - - - +
853A SER* 1.3 57.7 + - - +
855A GLY* 3.0 4.5 + - - -
856A ARG* 3.0 54.0 + - - +
1070A PHE* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849A PRO 2.8 22.3 + - - -
850A ARG* 3.2 27.7 + - - -
852A ALA* 1.3 73.0 - - - +
854A LEU* 1.3 56.8 + - - +
856A ARG* 3.9 18.7 - - - +
857A ARG* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY* 6.1 1.6 - - - -
710A ALA* 3.9 40.2 - - + +
713A ALA* 4.1 11.0 - - + -
714A VAL* 4.4 8.7 - - + -
850A ARG* 3.3 47.4 + - + +
851A ILE* 3.2 11.1 + - - +
852A ALA 3.2 0.8 - - - -
853A SER* 1.3 75.2 - - - +
855A GLY* 1.3 59.9 + - - +
856A ARG 3.3 0.4 - - - -
857A ARG* 3.3 7.2 + - + +
858A VAL* 3.1 30.7 + - - +
962A PRO* 3.4 34.3 - - + +
963A LEU 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ALA* 4.9 0.4 - - - +
840A MET 4.1 3.5 - - - +
843A LEU* 3.8 27.3 - - - +
844A ALA* 4.0 9.2 - - - -
851A ILE 3.0 7.1 + - - -
852A ALA 3.0 7.7 + - - -
854A LEU* 1.3 75.4 - - - +
856A ARG* 1.3 58.2 + - - +
858A VAL* 3.4 10.1 + - - +
859A LEU* 3.1 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ALA* 2.8 34.1 + - + +
845A LYS* 5.6 1.0 - - - +
849A PRO* 4.5 5.9 + - - +
852A ALA* 3.0 39.1 + - - +
853A SER* 3.9 16.4 - - - +
854A LEU 3.3 0.2 - - - -
855A GLY* 1.3 76.8 - - - +
857A ARG* 1.3 52.6 + - - +
859A LEU* 3.5 13.7 + - + +
860A SER* 2.7 30.9 + - - -
865A GLU* 5.3 0.5 - - - +
1070A PHE* 4.3 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A SER 3.2 14.7 + - - +
854A LEU* 3.3 12.5 + - + +
856A ARG* 1.3 74.1 - - - +
858A VAL* 1.3 64.6 + - - +
860A SER* 2.9 21.3 + - - -
861A ILE* 3.0 20.3 + - + +
959A SER 5.2 0.8 + - - -
960A LEU* 2.7 47.0 + - - +
961A LEU 4.4 1.2 + - - -
962A PRO* 3.7 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A ALA* 3.4 28.7 - - - +
716A LEU* 4.3 8.3 - - + -
717A ALA* 3.8 14.8 - - + -
720A ALA* 4.3 11.9 - - + -
840A MET* 3.6 39.5 - - + -
843A LEU* 5.6 2.2 - - + -
854A LEU 3.1 16.6 + - - +
855A GLY* 3.4 10.3 + - - +
857A ARG* 1.3 74.0 - - - +
859A LEU* 1.3 63.3 + - - +
861A ILE* 3.2 19.7 + - - +
862A ILE* 3.3 12.8 + - - +
962A PRO* 5.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 859 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A MET* 3.6 28.0 - - + -
841A PHE* 3.5 43.1 - - + +
844A ALA* 3.9 20.0 - - + -
855A GLY 3.1 15.4 + - - +
856A ARG* 3.5 14.4 - - + +
858A VAL* 1.3 77.2 - - - +
860A SER* 1.3 57.2 + - - +
862A ILE* 3.4 6.6 + - - +
863A GLY 3.2 7.6 + - - -
864A ILE* 2.9 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 860 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ARG 2.7 19.2 + - - -
857A ARG* 2.9 21.1 + - - -
859A LEU* 1.3 73.1 - - - +
861A ILE* 1.3 64.2 + - - +
862A ILE 3.2 0.7 - - - -
863A GLY* 3.3 11.9 + - - +
864A ILE 3.8 7.8 + - - +
865A GLU* 3.6 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 861 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A ALA* 4.1 6.1 - - + +
720A ALA* 4.5 7.0 - - + -
721A PHE* 4.2 35.9 - - + +
724A LYS* 3.6 26.7 - - - +
728A LYS* 5.7 0.3 + - - -
857A ARG* 3.0 38.7 + - - +
858A VAL* 3.2 16.4 + - - +
860A SER* 1.3 76.6 - - - +
862A ILE* 1.3 59.9 + - - +
863A GLY 3.8 0.2 + - - -
960A LEU* 4.8 11.9 - - + +
961A LEU* 3.9 25.4 - - + -
962A PRO* 4.0 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A ALA* 3.8 21.8 - - + +
724A LYS* 4.4 10.1 - - - +
727A LEU* 3.6 59.0 - - + +
728A LYS* 3.2 35.5 + - + +
731A ALA* 4.9 0.4 - - + -
837A VAL* 5.9 0.2 - - + -
840A MET* 3.7 20.2 - - + -
858A VAL 3.3 13.8 + - - +
859A LEU 3.7 8.3 - - - +
860A SER 3.2 0.4 - - - -
861A ILE* 1.3 78.4 - - - +
863A GLY* 1.3 55.8 + - - +
864A ILE* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LYS* 4.4 15.3 - - - +
859A LEU 3.2 2.2 + - - -
860A SER* 3.3 12.0 + - - -
861A ILE 3.4 0.2 - - - -
862A ILE* 1.3 80.6 - - - +
864A ILE* 1.3 63.7 + - - +
865A GLU* 4.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il